Any evidence that the majority of prehistorical sites had that?
It would be very difficult to prove the presence of holy water and relics that could easily get moved etc . We know the some of the sites that had churches built by or over but there isn't that many . There are also the odd marked rock or standing stone with an incised cross . I found one a couple of months ago . http://www.themodernantiquarian.com/site/15159/balnasuim.html